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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ), 'gf_id' => 'HOM05D001191', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001191' ), 'data_identifier' => 'HOM05D001191', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001191', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '524', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p67440' => 'bna', 'A06p08300' => 'bna', 'A06p38120' => 'bna', 'A08p33260' => 'bna', 'A08p36690' => 'bna', 'A09p05010' => 'bna', 'A10p03210' => 'bna', 'Aa31LG1G20110' => 'aar', 'Aa31LG2G8880' => 'aar', 'Aa31LG5G14910' => 'aar', 'Aa31LG8G10560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2735' => 'aag', 'Actinidia03291' => 'ach', 'Actinidia05510' => 'ach', 'Actinidia26907' => 'ach', 'Actinidia26908' => 'ach', 'Actinidia26909' => 'ach', 'Actinidia34625' => 'ach', 'Actinidia35953' => 'ach', 'Actinidia39992' => 'ach', 'Ah.06g191820' => 'amhyb', 'Ah.09g234830' => 'amhyb', 'Ah.15g094220' => 'amhyb', 'AL1G14500' => 'aly', 'AL1G22910' => 'aly', 'AL2G13850' => 'aly', 'AL3G14420' => 'aly', 'AL3G39010' => 'aly', 'Aqoxy2G03774' => 'aox', 'Aqoxy5G00184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1TFV27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4TB0JC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.52W6Q5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8UZ9VY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9U9X7L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A33MJY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6UPN1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J3UYT3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KZ8DRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TMAR50' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W2IB8V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YUD80W' => 'arhy', 'AT1G04780' => 'ath', 'AT1G11740' => 'ath', 'AT1G62050' => 'ath', 'AT3G04470' => 'ath', 'AT3G24210' => 'ath', 'ATR0736G008' => 'atr', 'ATR0757G067' => 'atr', 'ATR0787G046' => 'atr', 'ATR0794G117' => 'atr', 'ATR0807G119' => 'atr', 'Atru.chr10.2237' => 'acertr', 'Atru.chr2.996' => 'acertr', 'Atru.chr4.1763' => 'acertr', 'Atru.chr4.1764' => 'acertr', 'AUR62001294' => 'cqu', 'AUR62004831' => 'cqu', 'AUR62012716' => 'cqu', 'AUR62021939' => 'cqu', 'AUR62025679' => 'cqu', 'AUR62040918' => 'cqu', 'BcaB03g13236' => 'bca', 'BcaB03g13471' => 'bca', 'BcaB04g19635' => 'bca', 'BcaB04g20410' => 'bca', 'BcaC02g10513' => 'bca', 'BcaC04g23718' => 'bca', 'BcaC05g25043' => 'bca', 'BcaC06g30690' => 'bca', 'BcaC06g31878' => 'bca', 'BcaC06g35599' => 'bca', 'BcaC06g35600' => 'bca', 'BcaC07g36879' => 'bca', 'BcaNung02114' => 'bca', 'BolC1t03921H' => 'bol', 'BolC4t24349H' => 'bol', 'BolC5t29077H' => 'bol', 'BolC5t29726H' => 'bol', 'BolC7t41803H' => 'bol', 'BolC7t44545H' => 'bol', 'BolC8t46957H' => 'bol', 'BolC8t49122H' => 'bol', 'BolC9t53469H' => 'bol', 'BraA01t02731Z' => 'bra', 'BraA06t24029Z' => 'bra', 'BraA06t26726Z' => 'bra', 'BraA08t35245Z' => 'bra', 'BraA08t35572Z' => 'bra', 'BraA09t36140Z' => 'bra', 'BraA10t42595Z' => 'bra', 'C01p39680' => 'bna', 'C02p30940' => 'bna', 'C04p28050' => 'bna', 'C05p02960' => 'bna', 'C05p09870' => 'bna', 'C07p40090' => 'bna', 'C08p01490' => 'bna', 'C08p14930' => 'bna', 'C09p05420' => 'bna', 'CAN.G1465.13' => 'can', 'CAN.G24.4' => 'can', 'CAN.G500.71' => 'can', 'CAN.G569.3' => 'can', 'CAN.G706.20' => 'can', 'CANSAT54G0553' => 'cansat', 'CANSAT78G0228' => 'cansat', 'CARHR004170' => 'chi', 'CARHR050130' => 'chi', 'CARHR078610' => 'chi', 'CARHR078620' => 'chi', 'CARHR099940' => 'chi', 'CARHR185410' => 'chi', 'Carub.0001s0403' => 'cru', 'Carub.0001s1139' => 'cru', 'Carub.0002s0296' => 'cru', 'Carub.0003s0363' => 'cru', 'Carub.0003s2429' => 'cru', 'Ca_00666_v3' => 'car', 'Ca_09458_v3' => 'car', 'Ca_10019_v3' => 'car', 'Ca_10020_v3' => 'car', 'Ca_11840_v3' => 'car', 'Ca_11841_v3' => 'car', 'Ca_11843_v3' => 'car', 'Ca_29584_v3' => 'car', 'CBR_g48701' => 'cbr', 'Cc02_g08760' => 'ccan', 'Cc03_g07350' => 'ccan', 'Cc09_g01600' => 'ccan', 'CDE01G0179' => 'cde', 'CDE02G2394' => 'cde', 'CDE02G2891' => 'cde', 'CDE02G4344' => 'cde', 'CDE04G0351' => 'cde', 'CDE05G1650' => 'cde', 'CDE07G1765' => 'cde', 'CDE08G1204' => 'cde', 'Cfa000213' => 'cfa', 'Cfa006360' => 'cfa', 'Cfa014891' => 'cfa', 'Ciclev10004506m.g' => 'ccl', 'Ciclev10014683m.g' => 'ccl', 'Ciclev10019229m.g' => 'ccl', 'Ciclev10030460m.g' => 'ccl', 'CiPaw.01G125300' => 'cil', 'CiPaw.07G073300' => 'cil', 'CiPaw.09G092700' => 'cil', 'ClCG01G021930' => 'cla', 'ClCG03G009710' => 'cla', 'ClCG05G003520' => 'cla', 'ClCG11G010540' => 'cla', 'COL.COLO4_15494' => 'col', 'COL.COLO4_20308' => 'col', 'COL.COLO4_31784' => 'col', 'Cpa.g.sc152.21' => 'cpa', 'Cpa.g.sc306.7' => 'cpa', 'Cpa.g.sc59.103' => 'cpa', 'Cre08.g375150' => 'cre', 'CsaV3_1G045120' => 'csa', 'CsaV3_2G009850' => 'csa', 'CsaV3_3G011180' => 'csa', 'CsaV3_6G049000' => 'csa', 'CSS0028839' => 'camsi', 'CSS0035627' => 'camsi', 'CSS0036375' => 'camsi', 'CSS0042040' => 'camsi', 'CSS0049792' => 'camsi', 'DCAR_008157' => 'dca', 'DCAR_013313' => 'dca', 'DCAR_023089' => 'dca', 'Dinv13899' => 'din', 'Dinv18290' => 'din', 'Dinv24669' => 'din', 'Dinv29562' => 'din', 'Dinv38264' => 'din', 'Duzib106G1134' => 'dzi', 'Duzib128G0767' => 'dzi', 'Duzib151G0665' => 'dzi', 'Duzib160G0134' => 'dzi', 'Duzib177G1151' => 'dzi', 'Duzib212G0672' => 'dzi', 'Duzib235G0698' => 'dzi', 'Duzib268G0211' => 'dzi', 'ECA233G3804' => 'eca', 'ECA233G5041' => 'eca', 'ECA234G3111' => 'eca', 'ECA238G1509' => 'eca', 'ECA248G2892' => 'eca', 'EL10Ac4g08996' => 'bvu', 'EL10Ac7g18095' => 'bvu', 'EL10Ac8g20068' => 'bvu', 'Eucgr.D01334' => 'egr', 'Eucgr.H02830' => 'egr', 'Eucgr.H04225' => 'egr', 'Eucgr.L01449' => 'egr', 'FAN02G3257' => 'fan', 'FAN05G1058' => 'fan', 'FAN05G3318' => 'fan', 'FAN09G2028' => 'fan', 'FAN12G1095' => 'fan', 'FAN14G2989' => 'fan', 'FAN14G3839' => 'fan', 'FAN17G1655' => 'fan', 'FAN21G2981' => 'fan', 'FAN22G2391' => 'fan', 'FAN24G2663' => 'fan', 'FAN25G0740' => 'fan', 'FAN25G3711' => 'fan', 'FvH4_2g12060' => 'fve', 'FvH4_3g01950' => 'fve', 'FvH4_4g00280' => 'fve', 'FvH4_6g01790' => 'fve', 'Glyma.03G250400' => 'gma', 'Glyma.07G261200' => 'gma', 'Glyma.09G004100' => 'gma', 'Glyma.10G124300' => 'gma', 'Glyma.10G124500' => 'gma', 'Glyma.10G165700' => 'gma', 'Glyma.15G108300' => 'gma', 'Glyma.17G012800' => 'gma', 'Glyma.19G248000' => 'gma', 'Glyma.20G076500' => 'gma', 'Glyma.20G076600' => 'gma', 'Glyma.20G223500' => 'gma', 'Gohir.A02G024100' => 'ghi', 'Gohir.A06G148500' => 'ghi', 'Gohir.A09G202600' => 'ghi', 'Gohir.A10G121900' => 'ghi', 'Gohir.A11G246600' => 'ghi', 'Gohir.A11G246800' => 'ghi', 'Gohir.A13G161400' => 'ghi', 'Gohir.D02G031500' => 'ghi', 'Gohir.D06G154400' => 'ghi', 'Gohir.D09G196700' => 'ghi', 'Gohir.D10G144100' => 'ghi', 'Gohir.D11G256900' => 'ghi', 'Gohir.D11G257000' => 'ghi', 'Gohir.D13G174500' => 'ghi', 'Gohir.D13G174600' => 'ghi', 'Gorai.005G035000' => 'gra', 'Gorai.006G220100' => 'gra', 'Gorai.007G275300' => 'gra', 'Gorai.007G275400' => 'gra', 'Gorai.010G180500' => 'gra', 'Gorai.011G161000' => 'gra', 'Gorai.013G188000' => 'gra', 'GSVIVG01000517001' => 'vvi', 'GSVIVG01000518001' => 'vvi', 'GSVIVG01004564001' => 'vvi', 'GSVIVG01012718001' => 'vvi', 'HanXRQChr02g0059561' => 'han', 'HanXRQChr07g0194811' => 'han', 'HanXRQChr11g0342681' => 'han', 'HanXRQChr12g0367551' => 'han', 'HanXRQChr14g0454221' => 'han', 'Haze_04417' => 'cav', 'Haze_06808' => 'cav', 'Haze_11575' => 'cav', 'Haze_26486' => 'cav', 'Hma1.2p1_0749F.1_g212640' => 'hma', 'Hma1.2p1_1322F.1_g275480' => 'hma', 'HPP92_005005' => 'vpl', 'HPP92_012409' => 'vpl', 'HPP92_012888' => 'vpl', 'HPP92_012889' => 'vpl', 'HPP92_012913' => 'vpl', 'HPP92_014819' => 'vpl', 'Hund06904' => 'sun', 'Hund18547' => 'sun', 'Hund23464' => 'sun', 'Lalb_Chr01g0010771' => 'lal', 'Lalb_Chr02g0149061' => 'lal', 'Lalb_Chr04g0262101' => 'lal', 'Lalb_Chr06g0168261' => 'lal', 'Lalb_Chr13g0304261' => 'lal', 'Lalb_Chr19g0128861' => 'lal', 'Lalb_Chr19g0128941' => 'lal', 'Lj1g0026567' => 'lja', 'Lj2C268T1' => 'lonja', 'Lj2C44T14' => 'lonja', 'Lj3A580G62' => 'lonja', 'Lj3C564T0' => 'lonja', 'Lj3C564T1' => 'lonja', 'Lj4C620T7' => 'lonja', 'Lj4g0016327' => 'lja', 'Lj5g0021506' => 'lja', 'Lj6C615T4' => 'lonja', 'Lj6g0000638' => 'lja', 'Lj6g0005257' => 'lja', 'Lj6g0014704' => 'lja', 'Lj8P19T23' => 'lonja', 'Lsat_1_v5_gn_1_72301' => 'lsa', 'Lsat_1_v5_gn_4_60901' => 'lsa', 'Lsat_1_v5_gn_6_61621' => 'lsa', 'Lsat_1_v5_gn_8_24781' => 'lsa', 'Manes.03G149900' => 'mes', 'Manes.08G139900' => 'mes', 'Manes.09G147600' => 'mes', 'Manes.15G050900' => 'mes', 'Manes.16G006300' => 'mes', 'Mapoly0105s0047' => 'mpo', 'MBI02_g21880_MAGBIO' => 'mbi', 'MBI07_g21066_MAGBIO' => 'mbi', 'MBI07_g31084_MAGBIO' => 'mbi', 'MBI10_g16833_MAGBIO' => 'mbi', 'MBI18_g05902_MAGBIO' => 'mbi', 'MCO13G072' => 'mco', 'MD04G1002800' => 'mdo', 'MD04G1002900' => 'mdo', 'MD04G1230900' => 'mdo', 'MD05G1347900' => 'mdo', 'MD10G1322300' => 'mdo', 'MD12G1249200' => 'mdo', 'MD13G1284900' => 'mdo', 'MD13G1285000' => 'mdo', 'Medtr1g046580' => 'mtr', 'Medtr1g046930' => 'mtr', 'Medtr1g060820' => 'mtr', 'Medtr1g080310' => 'mtr', 'Medtr1g115930' => 'mtr', 'Medtr2g023450' => 'mtr', 'Medtr7g055655' => 'mtr', 'Medtr7g115580' => 'mtr', 'MELO3C006330.2' => 'cme', 'MELO3C007395.2' => 'cme', 'MELO3C008700.2' => 'cme', 'MELO3C010133.2' => 'cme', 'Migut.F00797' => 'egut', 'Migut.G00634' => 'egut', 'Migut.M01326' => 'egut', 'MSTRG.13137' => 'ama', 'MSTRG.15992' => 'ama', 'MSTRG.21952' => 'ama', 'MSTRG.27373' => 'ama', 'MSTRG.4216' => 'ama', 'MSTRG.7204' => 'ama', 'MSTRG.9829' => 'ama', 'Nitab4.5_0000306g0010' => 'nta', 'Nitab4.5_0000914g0040' => 'nta', 'Nitab4.5_0002827g0040' => 'nta', 'Nitab4.5_0002889g0070' => 'nta', 'Nitab4.5_0003965g0060' => 'nta', 'Nitab4.5_0004881g0080' => 'nta', 'Nitab4.5_0005074g0020' => 'nta', 'Nitab4.5_0015238g0010' => 'nta', 'Nn1g02870' => 'nnu', 'Nn1g03150' => 'nnu', 'Nn1g04707' => 'nnu', 'Nn1g07155' => 'nnu', 'Nn3g19721' => 'nnu', 'Nn3g19913' => 'nnu', 'Nn5g30198' => 'nnu', 'Nn6g33350' => 'nnu', 'Nn7g36913' => 'nnu', 'Oeu001461.4' => 'oeu', 'Oeu005632.1' => 'oeu', 'Oeu009477.1' => 'oeu', 'Oeu009478.1' => 'oeu', 'Oeu014927.1' => 'oeu', 'Oeu022358.1' => 'oeu', 'Oeu025270.1' => 'oeu', 'Oeu037762.1' => 'oeu', 'Oeu062215.1' => 'oeu', 'Oeu063489.2' => 'oeu', 'Os02g0810100' => 'osa', 'Os07g0436100' => 'osa', 'Os07g0512100' => 'osa', 'Peaxi162Scf00015g02913' => 'pax', 'Peaxi162Scf00047g01040' => 'pax', 'Peaxi162Scf00423g00131' => 'pax', 'Peaxi162Scf01204g00126' => 'pax', 'PGR004G1900' => 'pgr', 'PGR004G2839' => 'pgr', 'PGR083G0811' => 'pgr', 'PGSC0003DMG400009793' => 'stu', 'PGSC0003DMG400009794' => 'stu', 'PGSC0003DMG400023410' => 'stu', 'PGSC0003DMG400029625' => 'stu', 'PGSC0003DMG402016449' => 'stu', 'Phvul.003G079500' => 'pvu', 'Phvul.006G105000' => 'pvu', 'Phvul.006G149620' => 'pvu', 'Phvul.007G236300' => 'pvu', 'Phvul.007G236400' => 'pvu', 'Phvul.008G149506' => 'pvu', 'Phvul.L001760' => 'pvu', 'Potri.001G051400' => 'ptr', 'Potri.003G177000' => 'ptr', 'Potri.004G013500' => 'ptr', 'Potri.011G004500' => 'ptr', 'Potri.013G047500' => 'ptr', 'Potri.019G019700' => 'ptr', 'Pp3c14_11630' => 'ppa', 'Pp3c17_7170' => 'ppa', 'PRCOL_00004934' => 'pco', 'Prupe.1G002800' => 'ppe', 'Prupe.4G019600' => 'ppe', 'Prupe.6G350600' => 'ppe', 'Psat1g180040' => 'psa', 'Psat3g006800' => 'psa', 'Psat6g046960' => 'psa', 'Psat6g047000' => 'psa', 'Psat6g143480' => 'psa', 'PSO063G1068' => 'pso', 'PSO198G0035' => 'pso', 'PSO210G0812' => 'pso', 'PSO210G5078' => 'pso', 'PSO447G0141' => 'pso', 'PSO832G0703' => 'pso', 'PSO832G3950' => 'pso', 'QL03p029865' => 'qlo', 'QL05p073028' => 'qlo', 'QL06p023562' => 'qlo', 'RcHm_v2.0_Chr3g0449511' => 'rch', 'RcHm_v2.0_Chr4g0385121' => 'rch', 'RcHm_v2.0_Chr5g0002861' => 'rch', 'Rhsim02G0053800' => 'rsi', 'Rhsim05G0171900' => 'rsi', 'Rhsim09G0051400' => 'rsi', 'Rhsim09G0136700' => 'rsi', 'Rhsim13G0153200' => 'rsi', 'Sabra01G0035900' => 'sbr', 'Sabra03G0129700' => 'sbr', 'Sabra11G0003600' => 'sbr', 'SalBow1G2402' => 'sbo', 'SalBow1G4812' => 'sbo', 'SalBow2G1477' => 'sbo', 'SalBow3G3605' => 'sbo', 'SalBow8G0296' => 'sbo', 'Sc09g0004260' => 'sci', 'Sc24g0000180' => 'sci', 'Sed0000955' => 'sed', 'Sed0002786' => 'sed', 'Sed0004541' => 'sed', 'Sed0006580' => 'sed', 'Sed0008339' => 'sed', 'Sed0017375' => 'sed', 'Sed0027313' => 'sed', 'SEGI_09968' => 'sgi', 'SEGI_18547' => 'sgi', 'SEGI_29650' => 'sgi', 'SEGI_33104' => 'sgi', 'SGA_v2.0_scaffold2G01041' => 'sas', 'SGA_v2.0_scaffold57G20148' => 'sas', 'SGA_v2.0_scaffold89G27465' => 'sas', 'SHI02208' => 'shi', 'SHI18458' => 'shi', 'SHI18461' => 'shi', 'SHI35845' => 'shi', 'SMO119G0020' => 'smo', 'SMO164G0022' => 'smo', 'SMO180G0027' => 'smo', 'SMO340G0073' => 'smo', 'SMO340G0148' => 'smo', 'Solyc02g080610.4' => 'sly', 'Solyc05g054970.3' => 'sly', 'Solyc06g036620.1' => 'sly', 'Solyc06g036630.3' => 'sly', 'Solyc09g091560.3' => 'sly', 'Sopen02g025310' => 'spe', 'Sopen05g033430' => 'spe', 'Sopen06g012670' => 'spe', 'Sopen09g034480' => 'spe', 'Sp1g03620' => 'spa', 'Sp1g10350' => 'spa', 'Sp2g02510' => 'spa', 'Sp2g20000' => 'spa', 'Sp3g03320' => 'spa', 'Sp3g21740' => 'spa', 'TAR362G0794' => 'tar', 'TAR362G0827' => 'tar', 'TAR365G0039' => 'tar', 'TAR365G0968' => 'tar', 'TAR627G0590' => 'tar', 'TAR633G0199' => 'tar', 'TAR636G1041' => 'tar', 'THA.LOC104801039' => 'tha', 'THA.LOC104802848' => 'tha', 'THA.LOC104809503' => 'tha', 'THA.LOC104821614' => 'tha', 'THA.LOC104826117' => 'tha', 'Thecc.04G210100' => 'tca', 'Thecc.05G270200' => 'tca', 'Thecc.06G221900' => 'tca', 'Thhalv10002447m.g' => 'esa', 'Thhalv10003783m.g' => 'esa', 'Thhalv10007017m.g' => 'esa', 'Thhalv10009555m.g' => 'esa', 'Thhalv10023357m.g' => 'esa', 'TPR.G10102' => 'tpr', 'TPR.G11295' => 'tpr', 'TPR.G20874' => 'tpr', 'TPR.G22326' => 'tpr', 'TWI09G0068' => 'twi', 'TWI38G0086' => 'twi', 'TWI38G2238' => 'twi', 'TWI53G1992' => 'twi', 'TWI53G2062' => 'twi', 'TWI73G0331' => 'twi', 'unitig_21.g20236' => 'ugi', 'unitig_37.g12010' => 'ugi', 'unitig_744.g24520' => 'ugi', 'unitig_748.g8285' => 'ugi', 'unitig_748.g8286' => 'ugi', 'vmacro00504' => 'vma', 'vmacro10369' => 'vma', 'vmacro15509' => 'vma', 'vmacro19986' => 'vma', 'vmacro22534' => 'vma', 'vmacro23208' => 'vma', 'vmacro23209' => 'vma', 'VMungo0540G0337' => 'vmu', 'VMungo0540G0688' => 'vmu', 'VMungo0720G0155' => 'vmu', 'VMungo0720G2088' => 'vmu', 'VMungo0720G2793' => 'vmu', 'VMungo1215G1108' => 'vmu', 'Zm00001eb096850' => 'zma', 'Zm00001eb191680' => 'zma', 'Zm00001eb258480' => 'zma', 'Zm00001eb306100' => 'zma', 'Zm00001eb322560' => 'zma', 'Zm00001eb390880' => 'zma' ) $gf_id = 'HOM05D001191' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001191' ) $data_identifier = 'HOM05D001191' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 5, 'car' => (int) 8, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 12, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 3, 'lal' => (int) 7, 'lja' => (int) 6, 'lonja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 8, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 8, 'nnu' => (int) 9, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 7, 'sgi' => (int) 4, 'sas' => (int) 3, 'shi' => (int) 4, 'smo' => (int) 5, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 7, 'tha' => (int) 5, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 7, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb390880' $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